B2: How to change the center of rotation.
When a molecule is first displayed in Jmol the center of rotation is the center of mass of the molecule. If you want to view the entire molecule this is where it should be. However, you may want to zoom into a small region of the protein (e.g. the active site of an enzyme). If you then try to rotate the molecule, the region of interest may rotate out of view. To avoid this you can redefine the center of rotation using the following steps:
  1. Open the menu by clicking the right mouse button.
  2. Scroll down to "Set picking"
  3. Select "Center" from sub-menu.
  4. Click on the atom you wish to use as the new center.
  5. Reset the mouse click action by opening the menu, select "Set picking", and then select "Identify"
As you go through these steps the menus should appear as shown below the Jmol window.

To restore the center of rotation:

  1. Open the console (right click to bring up the menu)
  2. type "center" (no quotations)